Family Lineage
by Dragonball X Avalon
Summary: Jor-El is Clark's father. But Lara is not his mother. During his first visit to Earth, Jor-El fell in love with a young SHIELD agent. Fifteen years after he was found in a cornfield by Jonathan and Martha Kent, that agent comes to find the son she gave up. What effect will this have on the destiny of the World's Greatest Hero? Clark/Bobbi/Skye/Natasha pairing


**New York- 1989**

Maria Hill walked into her apartment, the level 4 SHIELD agent wanting nothing more than a whiskey and some sleep. The kill order on that stupid Russian billionaire had taken longer to execute than she had expected. And he was a bit more clingy than she had been led to believe. She understood that she was beautiful, and that he was one of the biggest womanizer's on the planet, at least according to her boss. But it felt like he had left permanent hand prints on her dress. Which was a shame because she actually liked this one.

" _Maria."_

She looked over to the sound of the noise, feeling her heart fall into her stomach. The voice was emanating from a silver crystal that hadn't been there when she left two days earlier. It was his voice. The voice she had wanted to hear more than any other, but at the same time prayed never to hear again. Because it meant the worst had happened.

" _My love, if you are hearing this then I am gone. My planet is gone. But our son is alive. He should have found his way to the family of Hiram Kent, the only one's aside from you to show me kindness. I know he will be well cared for, and that you will watch him from afar until the time is right. I love you my Maria."_

The crystal dimmed, and then faded from sight. Maria hardly noticed the tears that fell down her cheeks as she realized that he was gone. Jor-El, her first and only love was gone.

A few minutes later she stood up, wiping the tears from her eyes. She could cry later. Right now, she needed to ensure her son was safe.

 **Smallville Kansas- 1989**

"What are we going to tell people Martha? That we found him in a cornfield?" Jonathan asked as he looked at the baby in his wife's arms.

"We didn't find him. He found us." She replied softly.

Unknown to either one of them, Maria was watching the entire thing. She smiled, confident that her son would be safe.

"I love you son. I'll see you soon."

 **Smallville Kansas- Thirteen Years Later**

Clark Kent sighed as he threw the tennis ball against the wall of his 'Fortress of Solitude.' The last few weeks had seemed to be one screw up after another. First there had been the problems with Jor-El. The remnant of his biological father had told him that he was destined to rule the planet, and when Clark had refused to go along with his plan, he had been branded like cattle. Then he had destroyed the ship with Lionel's kryptonite key, which ended up doing more harm than good. His mother had lost her baby and he had put on his old class ring. He had run off to Metropolis and ended up working for Morgan Edge. When he had gotten bored of working for Edge, he had taken the money the mob boss had wanted him to steal. Edge had done the predictable thing and tried to kill Clark for double-crossing him. Needless to say, he hadn't succeeded, and Clark had burned his munition's factory to the ground. Meanwhile, Clark's dad had apparently made some deal with Jor-El and had used his temporary powers to convince his son to destroy the red kryptonite and come home. But the damage had been done. He and his parents were still walking around on eggshells and Lana didn't want anything to do with him. Not that he blamed her. Pete and Chloe were avoiding him. He was completely alone.

That last thought caused him to throw the tennis ball a bit harder than he intended, and it went through the wall. Clark made a mental note to fix the wall and went back to staring off into space.

He was so consumed in his thoughts that he didn't hear the footsteps coming up the stairs.

"Nice place."

Clark turned at the sound of the unknown woman's voice, feeling slightly annoyed that he hadn't heard her coming.

"Can I help you Miss-"

"I'm Maria Hill. I'm your mother."

As soon as the words left her mouth, Maria was cursing herself. Here she was the Deputy Director of SHIELD, and she had just talked like a rookie. It was rule number one of training. Make the mark comfortable with you before dropping the proverbial bomb. She could practically hear Fury chewing her out. But Clark wasn't some mark. He was her son. A son she had waited fifteen years to meet.

"I think you have me confused with someone else." He said, and she smiled.

"I promise you I don't. You're the spitting image of your father."

Seeing him looking at her like she was nuts, Hill decided to tell him what she knew.

"Your adopted parent's found you in a cornfield. In a spaceship. It was empty except for you and a piece of paper with your name on it. Clark. The name your father and I had agreed on."

"My father?" Clark asked, and Maria smiled.

"Jor-El."

Clark tensed, realizing that there had to be some truth to what Maria was saying. She knew far too much to simply be guessing.

Before Clark could respond, he heard the click of a shotgun. His father was standing behind Maria, his shotgun pressing into her back.

"Are you going to shoot me Mr. Kent?" Maria asked, sounding completely unconcerned. In truth, she could have taken Jonathan Kent down already. But cutting off her nose just to spite her face would be stupid.

"I'm thinking about it. I guess that just depends on what exactly you want with my son."

"Can we go downstairs and talk?" She asked calmly.

Jonathan slowly lowered his gun and turned around, walking down the stairs.

A few moments later, Maria and the Kent's sat around the dining room table.

"So you're Clark's biological mother." Martha said, and Maria nodded.

"I am."

"How is that possible? From what we've learned, Clark's DNA isn't compatible with human's."

"To be honest, I don't know about DNA. Science isn't my background. All I know is that fifteen years ago I met a man named Joe and fell in love with him. Nine months later, I gave birth to Clark."

She looked at the young man, once again struck by how much he looked like his father.

"The day you were born was the happiest day of my life. I still remember when the Doctor handed you to me. You looked up and smiled, and I promised right then that I would never let anything happen to you."

"Then why did you give me up?"

The word's came before Clark could stop them, but Maria didn't look offended. She just smiled sadly, having expected the question.

"I gave you up to protect you. When we met your father was here on a trip. It was tradition for Kryptonian's to go to another planet and learn about their culture once they turned twenty. He had to go back to Krypton after you were born, and he took you with him. A year later I saw him again. He told me that Krypton was doomed, and that he was working on a way to keep you safe. He wanted to send you to Earth, but we both knew he couldn't send you to me."

She sighed, and pulled out her badge, sliding it across the table.

"I'm the Assistant Director of the Strategic Homeland Intervention Enforcement and Logistics Division. SHIELD for short."

"Like the CIA?" Clark asked, and Maria chuckled.

"Not exactly. We're a step above. We're a global peacekeeping force."

"Yet you carry a weapon." Jonathan said, and Maria glared slightly.

" _Si vis pacem, para bellum._ " She replied calmly.

"If you want Peace, Prepare for War." Clark translated.

"Very good. Now Mr. Kent, I'm sure I don't have to tell you that there are terrible people in the world. Terrorists and psychopaths who want to kill innocent people just because they can. SHIELD exists to stop those threats. I have been fighting those threats my entire adult life. In the process I made enemies. People like Morgan Edge and some of the people Clark has handled over the last few years. People who would like nothing better than to use my son to get to me. I couldn't take the risk that your secret would be exposed Clark. That is why I gave you up. Not because I don't love you, because I do. And I couldn't be more proud of the man you have become. Using your gift's to help people...You're a hero." She said, and Clark shook his head.

"I'm no hero. I just want to do the right thing."

"And you have. You've saved a lot of lives."

"Why are you here Miss Hill?" Jonathan asked coldly. The woman may be Clark's biological mother, but he and Martha had raised him. And hell would freeze over before he would let some woman come and take his son.

"I'm here because I want to get to know my son. I don't want to take him away from his family Mr. Kent. I only want the chance to be a part of his life."

There was silence, and then Jonathan nodded. He may not trust Maria Hill, but she had kept his secret. And that earned her some points in the farmer's book.

"Can I talk to you for a minute?" Clark asked, and Maria looked towards the Kent's.

Jonathan looked at Martha, and she nodded.

"Alright. But dinner's in twenty minutes." He replied.

The two walked out to the barn, Clark unsure how to start.

"What do I call you?" He asked after a minute.

"Maria's fine. Take a breath Clark." She said, and he did just that, trying to sort his thoughts. He knew his father wouldn't approve about what he was going to ask, which is why he had decided to ask in private.

"You said that SHIELD is a peacekeeping force. That they help people. I'm assuming there was training involved?" He asked, and she nodded.

"Yes. Our agent's are trained to be the best."

"Would you train me?" He asked, and Maria sighed. She didn't want the life of a SHIELD agent for her son. But she also knew from her years of observation that he wouldn't stop helping people. She had failed in so much. But she would not fail I this.

"Clark, SHIELD isn't made up of cops. We kill people. I have killed people. You would most likely have to."

"In the last two years I have dealt with lunatics and nut jobs. I have seen some of the worst that humanity has to offer. And I have seen a woman I love die in my arms. I couldn't save her. I couldn't save my brother. I made my mother lose her baby. All this power, and I failed to save people when it mattered. Part of it was that I have relied too much on my abilities. I don't ever want to be in that position again. I don't want to lose anyone else I care about. So I am asking you, I am begging you to help me. Please."

She looked into his eyes, seeing the desperation there. But also the determination and desire to protect those he cared about. To make a difference in the world.

"I can get you a position at the Academy. But there are some conditions. Number one, no one knows that we are related. If anyone knows that I was your mother, it would put you in danger. Number two, you will carry a weapon at all times. And I expect you to give nothing but your best. And we have to get your parent's approval."

Clark nodded, not trusting himself to speak. The chances of Jonathan Kent letting him go join SHIELD weren't even slim. They were nonexistent.

 **The Next Morning**

"Be careful son. And call us when you get to New York." His mother said, and Clark nodded as he embraced his parent's.

"Take care of my son Maria." Jonathan said, and she nodded.

"He'll be safe. I promise you that."

When Clark had talked to his parent's the night before, their reaction had been exactly as he had predicted. Jonathan had hit the roof, refusing to allow his son to work for the government. But Clark had told his mom and dad what he had told Maria, and even though they hated the idea of Clark going away they knew he would never stop helping people. And as much as he hated to admit it, Jonathan knew that his son was destined for more than simply being a farmer. Looking into Maria's eyes, he knew that she would not let anyone hurt Clark. So he gave his consent. Clark would come back home on weekend's, but otherwise he would be in New York at SHIELD Academy. If his friend's asked, he had been accepted into a private school. And Maria would make sure that the paperwork was there to back it up.

The two got into Maria's car and headed to the airport, where a jet waited to take them to New York.

"Open the glove box. Take your pick." She said, and Clark opened the glove box, seeing a Beretta 92F, a Walther PPK and a Glock 19 sitting there.

Clark pulled out the Glock and shut the glove box. Maria nodded at his choice.

"Good call. Now tell me why you chose it."

"It has no safety. The others do. And you don't point a gun at something unless you're going to use it." He replied, and Maria smiled.

"Romanoff is going to love you."

"Who's Romanoff?" He asked, but Maria just smiled.

"You'll find out."

Clark just nodded, completely unaware of how important the woman in question would be to his future.

 **A/N: So this is an idea that was given to me by manufan2312, I hope you enjoy. Please read and review.**


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